"""
v0 script written by Myriam Benisty and Stefano Facchini (Feb 2st 2022)
v1 version adapted by Stefano Facchini and Myriam Benisty (Mar 2nd 2022)
v2 version adapted to include ACA data by Jane Huang and compacted code by Gianni Cataldi (May 19th 2022)
v3 (current version) includes EB alignment by Ryan Loomis and Richard Teague (Aug 2022)


This script is written for CASA 6.2.1.7. 
It can easily be adapted to other versions of CASA, e.g. by modifying the fixvis task to phaseshift task.

The numba package is used for the alignment script, but it is not necessary (it helps with the speed-up)

The scripts are written to be compatible mpicasa.
However, after testingthe exoALMA collaboration decided not to use mpicasa in any of the calibration scripts,
since they realized that differences in the results between casa and mpicasa could arise.

Person in charge for this source:
S. Facchini

"""

import os
import numpy as np
import shutil
import matplotlib
#increase the number of figures that can be open before issuing a warning
matplotlib.rcParams.update({'figure.max_open_warning':80})

#path to your local copy of the gihub repository
#(make sure to do a 'git pull' to have the most up-to-date version)
github_path = '/users/sfacchin/calibration_scripts'
import sys
sys.path.append(github_path)
import alignment
execfile(os.path.join(github_path,'reduction_utils_exoalma.py'))

prefix = 'HD_135344B'

data_folderpath = '/lustre/cv/projects/exoALMA/ALMA_PL_calibrated_data/HD_13534'
TM_names = {'LB':'TM1','SB':'TM2'}
PL_calibrated_vis = {key:os.path.join(data_folderpath,f'{TM_name}/calibrated_final.ms')
                     for key,TM_name in TM_names.items()}

for baseline_key,TM_name in TM_names.items():
    listobs(
        vis=PL_calibrated_vis[baseline_key],
        listfile=f'{prefix}_{TM_name}_calibrated_final.ms.txt',
        overwrite=True,
    )


# System properties.

incl =  15. # Cazzoletti+2018, Casassus+2021, rough estimate
PA = 62   # deg
v_sys = 7.1 # km/s; use the one from listobs

# Whether to run tclean in parallel or not.
use_parallel = False

spw_sets = {'SB':['25,27,29,31','92,94,96,98'],
            'LB':['25,27,29,31','88,90,92,94','108,110,112,114','128,130,132,134']}
fields = {'SB':'HD_135344B','LB':'HD_135344B'}


for baseline_key,vis in PL_calibrated_vis.items():
    split_all_obs(msfile=vis,nametemplate=f'{prefix}_{baseline_key}_EB')

number_of_EBs = {baseline_key:len(spw_set) for baseline_key,spw_set in spw_sets.items()}

for baseline_key,n_EB in number_of_EBs.items():
    for i in range(n_EB):
        vis = f'{prefix}_{baseline_key}_EB{i}.ms'
        listobs(
            vis=vis,
            listfile=f'{vis}.txt',
            overwrite=True,
        )

"""
Check that spws and field numbering is what you expect them to be now from the listobs files
In particular, make sure that there are 4 spws and that there is a single field with
field ID = 0
"""

# Line rest frequencies from splatalogue (https://splatalogue.online)
rest_freq_12CO = 345.79598990e9 #J=3-2
rest_freq_13CO = 330.58796530e9 #J=3-2 (ignoring splitting)
rest_freq_CS   = 342.88285030e9 #J=7-6

data_params_LB = {f'LB{i}': {'vis' : f'{prefix}_LB_EB{i}.ms',
                             'name' : f'LB_EB{i}',
                             'field' : fields['LB'],
                             'line_spws': np.array([0,2,3]), # list of spws containing lines
                             'line_freqs': np.array([rest_freq_13CO,rest_freq_CS,rest_freq_12CO]), #frequencies (Hz) corresponding to line_spws
                             'cont_spws': None,
                             'width_array': None,
                             }
                  for i in range(number_of_EBs['LB'])}

data_params_SB = {f'SB{i}': {'vis' : f'{prefix}_SB_EB{i}.ms',
                             'name' : f'SB_EB{i}',
                             'field' : fields['SB'],
                             'line_spws': np.array([0,2,3]), # list of spws containing lines
                             'line_freqs': np.array([rest_freq_13CO,rest_freq_CS,rest_freq_12CO]), #frequencies (Hz) corresponding to line_spws
                             'cont_spws': None,
                             'width_array': None,
                             }
                  for i in range(number_of_EBs['SB'])}


data_params = data_params_LB.copy()
data_params.update(data_params_SB)

figures_foldername = 'figures'
os.mkdir(figures_foldername)

def get_figures_folderpath(foldername):
    return os.path.join(figures_foldername,foldername)

def make_figures_folder(folderpath):
    if os.path.isdir(folderpath):
        print(f'going to deleted folder {folderpath} and its content')
        valid_answer = 'yes'
        answer = input(f'to confirm, type \'{valid_answer}\': ')
        if answer == valid_answer:
            shutil.rmtree(folderpath)
        else:
            print('aborting')
            return
    os.mkdir(folderpath)
    return folderpath

preselfcal_amp_figures_folder = get_figures_folderpath('1_preselfcal_amp_figures')
make_figures_folder(preselfcal_amp_figures_folder)

#adjust these plot ranges according to your data
plotranges = {'SB':[0,1000,0,0.3],#xmin,xmax,ymin,ymax
              'LB':[0,3500,0,0.3]}

for params in data_params.values():
    plot_filename = prefix+'_'+params['name']+'_chan-v-amp_preselfcal.png'
    plotms(vis=params['vis'],
            xaxis='channel',
            yaxis='amplitude',
            field=params['field'],
            ydatacolumn='data',
            avgtime='1e8',
            avgscan=True,
            avgbaseline=True,
            iteraxis='spw',
            #There is a bug in plotms that plots the data wrongly if there is unequal flagging
            #between the polarisations
            #the bug occurs if we plot amp and we average over baselines
            #thus we color by polarization such that
            #we easily identify this issue
            coloraxis='corr', 
            showgui = False,
            exprange='all',
            plotfile=os.path.join(preselfcal_amp_figures_folder,plot_filename)
            )
    baseline_key,_ = params['name'].split('_')
    plotms(vis=params['vis'],
           xaxis='UVdist',
           yaxis='amplitude',
           spw='1',
           field=params['field'],
           ydatacolumn='data',
           avgtime='1e8',
           avgscan=True,
           avgchannel='3840',
           showgui = False,
           plotrange=plotranges[baseline_key],
           plotfile=os.path.join(preselfcal_amp_figures_folder,
                                 prefix+'_'+params['name']+'_uvdist-v-amp_cont_spw_preselfcal.png')
           )


for params in data_params.values():
    flagchannels_string = get_flagchannels(ms_dict=params,output_prefix=prefix,
                                           velocity_range=np.array([-15.,15.])+v_sys)
    avg_cont(ms_dict=params,output_prefix=prefix,flagchannels=flagchannels_string,
             contspws=params['cont_spws'],width_array=params['width_array'])

"""
Double-check that the channels idenfied are at the center of the spws,
due to a potential issue with the data_desc_id key in the ms table of some programs
"""
# Flagchannels input string for LB_EB0: '0:833~3001, 2:797~3045, 3:781~3049'
# Flagchannels input string for LB_EB1: '0:833~3001, 2:797~3045, 3:781~3049'
# Flagchannels input string for LB_EB2: '0:833~3001, 2:797~3045, 3:781~3049'
# Flagchannels input string for LB_EB3: '0:833~3001, 2:797~3045, 3:781~3049'
# Flagchannels input string for SB_EB0: '0:837~3005, 2:792~3041, 3:789~3057'
# Flagchannels input string for SB_EB1: '0:836~3004, 2:793~3042, 3:788~3056'


preselfcal_initcont_amp_folder = get_figures_folderpath(
                                  '2_preselfcal_initcont_amp_figures')
make_figures_folder(preselfcal_initcont_amp_folder)

uv_ranges = {'LB':'125~150m','SB':'125~150m'}

for params in data_params.values():
    vis = prefix+'_'+params['name']+'_initcont.ms'
    baseline_key = params['name'].split('_')[0]
    plotms(vis=vis,
            xaxis='UVdist',
            overwrite=True,
            yaxis='amp',
            coloraxis='spw',
            avgtime='1e8',
            avgscan=True,
            showgui=False,
            plotrange=plotranges[baseline_key],
            plotfile=os.path.join(preselfcal_initcont_amp_folder,
                                  prefix+'_'+params['name']+'_uvdist-v-amp_initcont_preselfcal.png'))

    plotms(vis=vis,
            xaxis='time',
            yaxis='amp',
            avgspw=True,
            uvrange=uv_ranges[baseline_key],
            avgchannel='10000',
            avgbaseline=True,
            coloraxis='corr',
            showgui=False,
            overwrite=True,
            plotfile=os.path.join(preselfcal_initcont_amp_folder,
                                  prefix+'_'+params['name']+'_amp_v_time_initcont_preselfcal.png')
            )
#for SB, we see potential "waterfall features" (times where the amp suddently sharply decreases) in EB0
#we will try to fix this with self-cal


""" Define simple masks and clean scales for imaging """
mask_pa = PA #position angle of mask in degrees
mask_semimajor = 1.5 #semimajor axis of mask in arcsec
mask_semiminor = mask_semimajor*np.cos(incl/180.*np.pi) #semiminor axis of mask in arcsec
mask_ra = '15h15m48.409267s' #taken from listobs
mask_dec = '-37.09.16.54749'

mask = f'ellipse[[{mask_ra},{mask_dec}], [{mask_semimajor:.3f}arcsec,'\
            + f' {mask_semiminor:.3f}arcsec], {mask_pa:.1f}deg]'
# Cellsize: ~beam/6-7
cellsize =  {'LB':'0.015arcsec','SB':'0.040arcsec'}
# Image size: ~primary beam 1.22*lam/A = 32'' with A=12m (19 arcsec)
imsize = {'LB':1200,'SB':400}# primary beam
scales = {'LB':[0,8,15,30,80],'SB':[0,8,15,30]}

noise_annulus = f"annulus[[{mask_ra}, {mask_dec}],['4.arcsec', '6.arcsec']]"
thresholds = {'LB':'0.9mJy','SB':'4.9mJy'} #clean down to 6 sigma for phase cal

image_png_plot_sizes = [3,10] #sizes in arcsec of the zoomed and overview plots of the pngs

preselfcal_images_png_folder = get_figures_folderpath('3_preselfcal_images')
make_figures_folder(preselfcal_images_png_folder)

for baseline_key,params in zip(('LB','SB'),(data_params_LB,data_params_SB)):
    for EB_key,p in params.items():
        imagename = prefix+'_'+p['name']+'_initcont_image'
        tclean_wrapper(
                      vis=prefix+'_'+p['name']+'_initcont.ms',
                      imagename=imagename,
                      deconvolver='multiscale',
                      scales=scales[baseline_key],
                      mask=mask,
                      threshold=thresholds[baseline_key],
                      cellsize=cellsize[baseline_key],
                      imsize=imsize[baseline_key],
                      parallel=use_parallel,
                      savemodel='modelcolumn'
                    )
        estimate_SNR(f'{imagename}.image',disk_mask=mask,noise_mask=noise_annulus)
        rms = imstat(imagename=f'{imagename}.image',region=noise_annulus)['rms'][0]
        params[EB_key]['rms'] = rms
        generate_image_png(f'{imagename}.image',plot_sizes=image_png_plot_sizes,
                            color_scale_limits=[-3*rms,10*rms],
                            save_folder=preselfcal_images_png_folder)

#HD_135344B_LB_EB0_initcont_image.image
#Beam 0.118 arcsec x 0.106 arcsec (-10.50 deg)
#Flux inside disk mask: 426.13 mJy
#Peak intensity of source: 9.63 mJy/beam
#rms: 1.24e-01 mJy/beam
#Peak SNR: 77.81

#HD_135344B_LB_EB1_initcont_image.image
#Beam 0.112 arcsec x 0.098 arcsec (77.31 deg)
#Flux inside disk mask: 439.07 mJy
#Peak intensity of source: 8.97 mJy/beam
#rms: 1.20e-01 mJy/beam
#Peak SNR: 74.97

#HD_135344B_LB_EB2_initcont_image.image
#Beam 0.138 arcsec x 0.098 arcsec (87.68 deg)
#Flux inside disk mask: 402.48 mJy
#Peak intensity of source: 9.82 mJy/beam
#rms: 2.63e-01 mJy/beam
#Peak SNR: 37.40

#HD_135344B_LB_EB3_initcont_image.image
#Beam 0.135 arcsec x 0.094 arcsec (-77.11 deg)
#Flux inside disk mask: 433.83 mJy
#Peak intensity of source: 10.31 mJy/beam
#rms: 1.39e-01 mJy/beam
#Peak SNR: 73.92

#HD_135344B_SB_EB0_initcont_image.image
#Beam 0.350 arcsec x 0.251 arcsec (-85.34 deg)
#Flux inside disk mask: 466.50 mJy
#Peak intensity of source: 52.90 mJy/beam
#rms: 3.78e-01 mJy/beam
#Peak SNR: 139.98

#HD_135344B_SB_EB1_initcont_image.image
#Beam 0.527 arcsec x 0.425 arcsec (78.19 deg)
#Flux inside disk mask: 393.05 mJy
#Peak intensity of source: 95.31 mJy/beam
#rms: 7.72e-01 mJy/beam
#Peak SNR: 123.48

######
# SELF-CAL INDIVIDUAL EBs
######
""" Self-calibration parameters """
single_EB_contspws = '0~3'
single_EB_spw_mapping = [0,0,0,0]

individual_EB_selfcal_shift_folder = get_figures_folderpath(
                                                   '4_individual_EB_selfcal_and_shift_figures')
make_figures_folder(individual_EB_selfcal_shift_folder)

""" One round of phase-only self-cal """
for params in data_params.values():
    vis = prefix+'_'+params['name']+'_initcont.ms'
    single_EB_p1 = prefix+'_'+params['name']+'_initcont.p1'
    os.system(f'rm -rf {single_EB_p1}')
    gaincal(vis=vis,caltable=single_EB_p1,gaintype='T',spw=single_EB_contspws,
            combine='scan,spw',calmode='p',solint='inf',minsnr=4,minblperant=3)
    """ Print calibration png file """
    plotfilename = prefix+'_'+params['name']\
                        +'_initcont_gain_p1_phase_vs_time.png'
    plotms(single_EB_p1,xaxis='time',yaxis='GainPhase',overwrite=True,showgui=False,
           plotfile=os.path.join(individual_EB_selfcal_shift_folder,plotfilename))
    """ Apply the solutions """
    applycal(vis=vis,spw=single_EB_contspws,spwmap=single_EB_spw_mapping,
             gaintable=[single_EB_p1],interp='linearPD',applymode='calonly',calwt=True)
    split(vis=vis,outputvis=prefix+'_'+params['name']+'_initcont_selfcal.ms',
          datacolumn='corrected')

# No flagging seen in any dataset

### Image self-cal'd EBs ###

for baseline_key,params in zip(('LB','SB'),(data_params_LB,data_params_SB)):
    for p in params.values():
        imagename = prefix+'_'+p['name']+'_initcont_selfcal_image'
        tclean_wrapper(vis=prefix+'_'+p['name']+'_initcont_selfcal.ms',
                        imagename=imagename,
                        deconvolver='multiscale',
                        scales=scales[baseline_key],
                        mask=mask,
                        threshold=thresholds[baseline_key],
                        cellsize=cellsize[baseline_key],
                        imsize=imsize[baseline_key],
                        parallel=use_parallel,
                        )
        output_image = f'{imagename}.image'
        estimate_SNR(output_image,disk_mask=mask,noise_mask=noise_annulus)
        rms = p['rms']
        generate_image_png(image=output_image,plot_sizes=image_png_plot_sizes,
                           color_scale_limits=[-3*rms,10*rms],
                           save_folder=individual_EB_selfcal_shift_folder)


for baseline_key,params in zip(('LB','SB'),(data_params_LB,data_params_SB)):
    for p in params.values():
        imagename = prefix+'_'+p['name']+'_initcont_selfcal_image'
        #ratio image, to be compared to the ratio image after alignment
        ref_image = f'{prefix}_{baseline_key}_EB0_initcont_selfcal_image.image'
        ref_rms = params[f'{baseline_key}0']['rms']
        ratio_image = imagename+'.ratio'
        os.system(f'rm -rf {ratio_image}')
        immath(imagename=[ref_image,imagename+'.image'],mode='evalexpr',
               outfile=ratio_image,expr=f'iif(IM0 > 3*{ref_rms}, IM1/IM0, 0)')
        generate_image_png(ratio_image,plot_sizes=[2*mask_semimajor,2*mask_semimajor],
                           color_scale_limits=[0.5,1.5],image_units='ratio',
                           save_folder=individual_EB_selfcal_shift_folder)

#HD_135344B_LB_EB0_initcont_selfcal_image.image
#Beam 0.118 arcsec x 0.106 arcsec (-10.50 deg)
#Flux inside disk mask: 426.97 mJy
#Peak intensity of source: 9.80 mJy/beam
#rms: 1.03e-01 mJy/beam
#Peak SNR: 95.10

#HD_135344B_LB_EB1_initcont_selfcal_image.image
#Beam 0.112 arcsec x 0.098 arcsec (77.31 deg)
#Flux inside disk mask: 438.77 mJy
#Peak intensity of source: 9.07 mJy/beam
#rms: 9.23e-02 mJy/beam
#Peak SNR: 98.19

#HD_135344B_LB_EB2_initcont_selfcal_image.image
#Beam 0.138 arcsec x 0.098 arcsec (87.68 deg)
#Flux inside disk mask: 408.09 mJy
#Peak intensity of source: 10.45 mJy/beam
#rms: 1.66e-01 mJy/beam
#Peak SNR: 62.90

#HD_135344B_LB_EB3_initcont_selfcal_image.image
#Beam 0.135 arcsec x 0.094 arcsec (-77.11 deg)
#Flux inside disk mask: 436.30 mJy
#Peak intensity of source: 10.36 mJy/beam
#rms: 9.91e-02 mJy/beam
#Peak SNR: 104.53

#HD_135344B_SB_EB0_initcont_selfcal_image.image
#Beam 0.350 arcsec x 0.251 arcsec (-85.34 deg)
#Flux inside disk mask: 472.56 mJy
#Peak intensity of source: 54.26 mJy/beam
#rms: 2.61e-01 mJy/beam
#Peak SNR: 207.76

#HD_135344B_SB_EB1_initcont_selfcal_image.image
#Beam 0.527 arcsec x 0.425 arcsec (78.19 deg)
#Flux inside disk mask: 419.88 mJy
#Peak intensity of source: 101.10 mJy/beam
#rms: 1.87e-01 mJy/beam
#Peak SNR: 540.73

######
# ALIGN DATA (go from *initcont_selfcal.ms to *initcont_shift.ms)
######

# Select the LB EB to act as the reference (usually the best SNR one).

reference_for_LB_alignment = f'{prefix}_LB_EB1_initcont_selfcal.ms'
assert 'LB' in reference_for_LB_alignment,\
            'you need to choose an LB EB for alignment of LB'

alignment_offsets = {}

# All the other EBs will be aligned to the reference EB
# We also include the reference EB itself to make sure the coordinate changes are
# copied over.

offset_LB_EBs = ['{}_{}_initcont_selfcal.ms'.format(prefix, params['name'])
                 for params in data_params_LB.values()]

#select the continuum spw with the large bandwidth
continuum_spw_id = 1
# Find the relative offsets and update the phase centers for all offset_EBs.
npix = 1024
cell_size = 0.01
alignment.align_measurement_sets(reference_ms=reference_for_LB_alignment,
                                 align_ms=offset_LB_EBs,npix=npix,cell_size=cell_size,
                                 spwid=continuum_spw_id)

#New coordinates for HD_135344B_LB_EB0_initcont_selfcal.ms
#requires a shift of [-0.017116,0.00088458]

#New coordinates for HD_135344B_LB_EB1_initcont_selfcal.ms
#no shift, reference MS.

#New coordinates for HD_135344B_LB_EB2_initcont_selfcal.ms
#requires a shift of [0.029619,0.0025547]

#New coordinates for HD_135344B_LB_EB3_initcont_selfcal.ms
#requires a shift of [-0.031739,-0.0017999]


#insert offsets from the alignment output
alignment_offsets['LB_EB0'] = [-0.017116,0.00088458]
alignment_offsets['LB_EB1'] = [0.,0.]
alignment_offsets['LB_EB2'] = [0.029619,0.0025547]
alignment_offsets['LB_EB3'] = [-0.031739,-0.0017999]

shifted_LB_EBs = [EB.replace('.ms','_shift.ms') for EB in offset_LB_EBs]

#to check if alignment worked, calculate shift again and verify that shifts are small (i.e.
#a fraction of the cell size):

for shifted_ms in shifted_LB_EBs:
    if shifted_ms == reference_for_LB_alignment.replace('.ms','_shift.ms'):
        #for some reason the fitter fails when computing the offset of an EB to itself,
        #so we skip the ref EB
        continue
    offset = alignment.find_offset(reference_ms=reference_for_LB_alignment,
                                   offset_ms=shifted_ms,npix=npix,cell_size=cell_size,
                                   spwid=continuum_spw_id)
    print(f'#offset for {shifted_ms}: ',offset)

#offset for HD_135344B_LB_EB0_initcont_selfcal_shift.ms:  [-0.00051163 -0.0001141 ]
#offset for HD_135344B_LB_EB2_initcont_selfcal_shift.ms:  [2.86198900e-05 1.19846033e-04]
#offset for HD_135344B_LB_EB3_initcont_selfcal_shift.ms:  [-0.00067771 -0.000353  ]


# Merge shifted LB EBs for aligning SB EBs
LB_concat_shifted = f'{prefix}_LB_concat_shifted.ms'
os.system(f'rm -rf {LB_concat_shifted}')
concat(vis=shifted_LB_EBs,concatvis=LB_concat_shifted,dirtol='0.1arcsec',
       copypointing=False)


# Align SB EBs to concat shifted LB EBs
reference_for_SB_alignment = LB_concat_shifted

offset_SB_EBs = ['{}_{}_initcont_selfcal.ms'.format(prefix, params['name'])
                 for params in data_params_SB.values()]

alignment.align_measurement_sets(reference_ms=reference_for_SB_alignment,
                                 align_ms=offset_SB_EBs,npix=npix,cell_size=cell_size,
                                 spwid=continuum_spw_id)

#New coordinates for HD_135344B_SB_EB0_initcont_selfcal.ms
#requires a shift of [-0.013165,-0.029931]
#New coordinates for HD_135344B_SB_EB1_initcont_selfcal.ms
#requires a shift of [-0.020615,0.016539]


alignment_offsets['SB_EB0'] = [-0.013165,-0.029931]
alignment_offsets['SB_EB1'] = [-0.020615,0.016539]

shifted_SB_EBs = [EB.replace('.ms','_shift.ms') for EB in offset_SB_EBs]

#check by calculating offset again
for shifted_ms in shifted_SB_EBs:
    offset = alignment.find_offset(reference_ms=reference_for_SB_alignment,
                                   offset_ms=shifted_ms,npix=npix,cell_size=cell_size,
                                   spwid=continuum_spw_id)
    print(f'#offset for {shifted_ms}: ',offset)
#offset for HD_135344B_SB_EB0_initcont_selfcal_shift.ms:  [-0.00068715 -0.00025995]
#offset for HD_135344B_SB_EB1_initcont_selfcal_shift.ms:  [-0.00040394 -0.00012193]


# Remove the '_selfcal' part of the names to match the naming convention below.
for shifted_EB in shifted_LB_EBs+shifted_SB_EBs:
    os.system('mv {} {}'.format(shifted_EB, shifted_EB.replace('_selfcal', '')))


""" Check that the images are indeed aligned after the shift """

for baseline_key,params in zip(('LB','SB'),(data_params_LB,data_params_SB)):
    for p in params.values():
        imagename = prefix+'_'+p['name']+'_initcont_shift_image'
        tclean_wrapper(vis=prefix+'_'+p['name']+'_initcont_shift.ms',
                        imagename=imagename,
                        deconvolver='multiscale',
                        scales=scales[baseline_key],
                        mask=mask,
                        threshold=thresholds[baseline_key],
                        cellsize=cellsize[baseline_key],
                        imsize=imsize[baseline_key],
                        parallel=use_parallel,
                      )
        estimate_SNR(f'{imagename}.image',disk_mask=mask,
                     noise_mask=noise_annulus)
        rms = p['rms']
        generate_image_png(f'{imagename}.image',plot_sizes=image_png_plot_sizes,
                           color_scale_limits=[-3*rms,10*rms],
                           save_folder=individual_EB_selfcal_shift_folder)

for baseline_key,params in zip(('LB','SB'),(data_params_LB,data_params_SB)):
    for p in params.values():
        imagename = prefix+'_'+p['name']+'_initcont_shift_image'
        ref_image = f'{prefix}_{baseline_key}_EB0_initcont_shift_image.image'
        ref_rms = params[f'{baseline_key}0']['rms']
        ratio_image = imagename+'.ratio'
        os.system(f'rm -rf {ratio_image}')
        immath(imagename=[ref_image,imagename+'.image'],mode='evalexpr',
               outfile=ratio_image,expr=f'iif(IM0 > 3*{ref_rms}, IM1/IM0, 0)')
        generate_image_png(ratio_image,plot_sizes=[2*mask_semimajor,2*mask_semimajor],
                           color_scale_limits=[0.5,1.5],image_units='ratio',
                           save_folder=individual_EB_selfcal_shift_folder)


""" Now that everything is aligned, we inspect the flux calibration. """

for params in data_params.values():
    msfile = prefix+'_'+params['name']+'_initcont_shift.ms'
    export_MS(msfile) #export MS contents into Numpy save files

""" Plot deprojected visibility profiles for all data together """
list_npz_files = []
for baseline_key,n_EB in number_of_EBs.items():
    list_npz_files += [f'{prefix}_{baseline_key}_EB{i}_initcont_shift.vis.npz'
                       for i in range(n_EB)]

deprojected_vis_profiles_folder = get_figures_folderpath('5_deprojected_vis_profiles')
make_figures_folder(deprojected_vis_profiles_folder)

plot_deprojected(filelist=list_npz_files,
                 fluxscale=[1.]*(number_of_EBs['LB']+number_of_EBs['SB']),PA=PA,
                 incl=incl,show_err=True,
                 plot_label=os.path.join(deprojected_vis_profiles_folder,
                                         f'{prefix}_flux_scale_EB_preselfcal.png'))

flux_comparison_folder = get_figures_folderpath('6_flux_comparisons')
make_figures_folder(flux_comparison_folder)

#we choose an EB to compare the flux scaling; if possible the best SB EB
#since SB_EB0 seems to have some de-coherence, we use SB_EB1
flux_ref_EB = 'SB_EB1'

for params in data_params.values():
    plot_label = os.path.join(flux_comparison_folder,
                              'flux_comparison_'+params['name']+f'_to_{flux_ref_EB}.png')
    estimate_flux_scale(reference=f'{prefix}_{flux_ref_EB}_initcont_shift.vis.npz',
                        comparison=prefix+'_'+params['name']+'_initcont_shift.vis.npz',
                        incl=incl, PA=PA,plot_label=plot_label)

#The ratio of the fluxes of HD_135344B_LB_EB0_initcont_shift.vis.npz to
#HD_135344B_SB_EB1_initcont_shift.vis.npz is 0.99071
#The scaling factor for gencal is 0.995 for your comparison measurement
#The error on the weighted mean ratio is 4.717e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_LB_EB1_initcont_shift.vis.npz to
#HD_135344B_SB_EB1_initcont_shift.vis.npz is 1.03665
#The scaling factor for gencal is 1.018 for your comparison measurement
#The error on the weighted mean ratio is 4.600e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_LB_EB2_initcont_shift.vis.npz to
#HD_135344B_SB_EB1_initcont_shift.vis.npz is 0.93494
#The scaling factor for gencal is 0.967 for your comparison measurement
#The error on the weighted mean ratio is 3.780e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_LB_EB3_initcont_shift.vis.npz to
#HD_135344B_SB_EB1_initcont_shift.vis.npz is 1.01423
#The scaling factor for gencal is 1.007 for your comparison measurement
#The error on the weighted mean ratio is 3.927e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_SB_EB0_initcont_shift.vis.npz to
#HD_135344B_SB_EB1_initcont_shift.vis.npz is 1.09747
#The scaling factor for gencal is 1.048 for your comparison measurement
#The error on the weighted mean ratio is 1.969e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_SB_EB1_initcont_shift.vis.npz to
#HD_135344B_SB_EB1_initcont_shift.vis.npz is 1.00000
#The scaling factor for gencal is 1.000 for your comparison measurement
#The error on the weighted mean ratio is 1.680e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor


# Results are not clear, potential de-coherence in both SB EBs, we try LB_EB0 as reference...
flux_ref_EB = 'LB_EB0'

for params in data_params.values():
    plot_label = os.path.join(flux_comparison_folder,
                              'flux_comparison_'+params['name']+f'_to_{flux_ref_EB}.png')
    estimate_flux_scale(reference=f'{prefix}_{flux_ref_EB}_initcont_shift.vis.npz',
                        comparison=prefix+'_'+params['name']+'_initcont_shift.vis.npz',
                        incl=incl, PA=PA,plot_label=plot_label)

#The ratio of the fluxes of HD_135344B_LB_EB0_initcont_shift.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 1.00000
#The scaling factor for gencal is 1.000 for your comparison measurement
#The error on the weighted mean ratio is 6.256e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_LB_EB1_initcont_shift.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 1.04113
#The scaling factor for gencal is 1.020 for your comparison measurement
#The error on the weighted mean ratio is 6.405e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_LB_EB2_initcont_shift.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 0.93919
#The scaling factor for gencal is 0.969 for your comparison measurement
#The error on the weighted mean ratio is 5.684e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_LB_EB3_initcont_shift.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 1.01986
#The scaling factor for gencal is 1.010 for your comparison measurement
#The error on the weighted mean ratio is 5.819e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_SB_EB0_initcont_shift.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 1.08407
#The scaling factor for gencal is 1.041 for your comparison measurement
#The error on the weighted mean ratio is 5.154e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_SB_EB1_initcont_shift.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 0.98388
#The scaling factor for gencal is 0.992 for your comparison measurement
#The error on the weighted mean ratio is 4.683e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#LB_EB1 and LB_EB2 values are >4% compared to LB_EB0. SB_EB0 data is off, possibly due
#to decoherence, so we do not re-scale SB_EB0 now

rescale_flux(vis=prefix+'_LB_EB1_initcont_shift.ms', gencalparameter=[1.020])
rescale_flux(vis=prefix+'_LB_EB2_initcont_shift.ms', gencalparameter=[0.969])
#Splitting out rescaled values into new MS: HD_135344B_LB_EB1_initcont_shift_rescaled.ms
#Splitting out rescaled values into new MS: HD_135344B_LB_EB2_initcont_shift_rescaled.ms

"""

SB has overlapping uv ranges with both ACA and LB, so
we select an SB EB as the reference for flux scaling.

In case this source does not have ACA data, simply ignore the ACA steps in the list below.
 
If all SB EBs suffer from decoherence and cannot be used, see below

We correct flux differences >4%, if phase noise looks reasonable

If you need to re-scale fluxes, use command:
rescale_flux(vis=prefix+'_LB_EB0_initcont_shift.ms', gencalparameter=[1.044])

The general procedure is as follows:
1) check flux scaling, and if flux differences are >4%, re-scale the fluxes unless
    there is clear de-coherence (e.g. seen as a systematic decrease of scaling with UV distance)
2) do not scale those EBs with phase decoherence. Proceed with self-cal following the steps below 
   to the point that those EBs are self calibrated
3) check flux scaling again
4) if no flux scaling has been applied in 1), and you now still see a flux offset, then
    apply the flux scaling determined in step 3) to the non-self caled EBs
    and repeat the self-cal

If all SB EBs suffer from phase decoherence and cannot be used as the reference
for flux scaling:
1) concat ACA data and self-cal them in phase
2) concat them to SB data and self-cal them in phase
3) check flux offsets
4) if there are flux offsets, go back to 1), but before re-starting the process apply
    the corrections to the non-self caled ACA and SB data, and re-do steps 1) - 3).
    For this you should add additional code (essentially copy/paste the code from the first
    iteration) that repeats steps 1-3, but saves all output with different filenames. Remember
    to use the right filenames when you continue the script after step 6
5) Check flux offsets of LB EBs to a correct SB EB
6) concat LB data to ACA+SB and continue with script

"""
#For HD135344B, we see clear decoherence, so we proceed with SB self-cal without flux-scaling

############ START of SB self-cal ############
#for phase cal, clean down to 6 sigma

SB_selfcal_folder = get_figures_folderpath('7_selfcal_SB_figures')
make_figures_folder(SB_selfcal_folder)

SB_cont_p0 = prefix+'_SB_contp0'
os.system('rm -rf %s.ms*' %SB_cont_p0)

concat(vis=[f'{prefix}_SB_EB{i}_initcont_shift.ms' for i in range(number_of_EBs['SB'])],
       concatvis=SB_cont_p0+'.ms',dirtol='0.1arcsec',copypointing=False)

listobs(vis=SB_cont_p0+'.ms',listfile=SB_cont_p0+'.ms.txt',overwrite=True)

"""Define new SB mask using new center read from listobs"""
mask_ra = '15h15m48.412300s'
mask_dec = '-37.09.16.53940'

SB_mask= f'ellipse[[{mask_ra},{mask_dec}], [{mask_semimajor:.3f}arcsec,'\
         +f'{mask_semiminor:.3f}arcsec], {mask_pa:.1f}deg]'

noise_annulus_SB = f"annulus[[{mask_ra}, {mask_dec}],['4.arcsec', '6.arcsec']]"

SB_tclean_wrapper_kwargs = {'mask':SB_mask,'deconvolver':'multiscale',
                            'scales':scales['SB'],'savemodel':'modelcolumn',
                            'imsize':imsize['SB'],'cellsize':cellsize['SB'],
                            'robust':0.5,'interactive':False,
                            'parallel':use_parallel,'gridder':'standard'}

#go down to ~6 sigma
tclean_wrapper(vis=SB_cont_p0+'.ms',imagename = SB_cont_p0,
               threshold = '0.78mJy', **SB_tclean_wrapper_kwargs)
estimate_SNR(SB_cont_p0+'.image', disk_mask = SB_mask,noise_mask = noise_annulus_SB)
#HD_135344B_SB_contp0.image
#Beam 0.394 arcsec x 0.297 arcsec (-89.11 deg)
#Flux inside disk mask: 441.62 mJy
#Peak intensity of source: 65.99 mJy/beam
#rms: 1.29e-01 mJy/beam
#Peak SNR: 513.35

rms_SB = imstat(imagename = SB_cont_p0+'.image',region = noise_annulus_SB)['rms'][0]
generate_image_png(SB_cont_p0+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB,10*rms_SB],
                   save_folder=SB_selfcal_folder)

""" Look for references antennas from weblog, and pick the first that are listed, overlapping with all EBs """
# both EBs: DA63, DA57, DA08

""" Get station numbers """
for ref_ant in ('DA63','DA57'):
    get_station_numbers(SB_cont_p0+'.ms',ref_ant)
#Observation ID 0: DA63@A035
#Observation ID 1: DA63@A035
#Observation ID 0: DA57@A001
#Observation ID 1: DA57@A001

SB_contspws = '0~7'
SB_refant   = 'DA63@A035, DA57@A001'
SB_spw_mapping = [0,0,0,0,4,4,4,4]

#First round
SB_p1 = prefix+'_SB_p1'
os.system('rm -rf '+SB_p1)
gaincal(vis=SB_cont_p0+'.ms',caltable=SB_p1,
        gaintype='G', spw=SB_contspws,refant=SB_refant, combine='scan,spw',
        calmode='p', solint='inf', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_p1,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_p1,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_selfcal_folder,
                             f'{prefix}_SB_p1_gain_phase_vs_time.png')
       )

""" Apply the solutions """
applycal(vis=SB_cont_p0+'.ms',spw=SB_contspws,
         spwmap=SB_spw_mapping,gaintable=[SB_p1], interp='linearPD',
         calwt=True, applymode='calonly')

SB_cont_p1 = SB_cont_p0.replace('p0','p1')
os.system('rm -rf %s.ms*' % SB_cont_p1)
split(vis=SB_cont_p0+'.ms',outputvis=SB_cont_p1+'.ms', datacolumn='corrected')

#again threshold should be ~6sigma
tclean_wrapper(vis=SB_cont_p1+'.ms',imagename = SB_cont_p1,
               threshold = '0.78mJy', **SB_tclean_wrapper_kwargs)
estimate_SNR(SB_cont_p1+'.image',disk_mask=SB_mask,noise_mask=noise_annulus_SB)
generate_image_png(SB_cont_p1+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB,10*rms_SB],
                   save_folder=SB_selfcal_folder)
#HD_135344B_SB_contp1.image
#Beam 0.394 arcsec x 0.297 arcsec (-89.11 deg)
#Flux inside disk mask: 441.61 mJy
#Peak intensity of source: 66.00 mJy/beam
#rms: 1.27e-01 mJy/beam
#Peak SNR: 520.24


#Second round
SB_p2 = SB_p1.replace('p1','p2')
os.system('rm -rf '+SB_p2)
gaincal(vis=SB_cont_p1+'.ms',caltable=SB_p2,
        gaintype='T',spw=SB_contspws,refant=SB_refant, combine='scan,spw',
        calmode='p', solint='360s', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_p2,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_p2,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_selfcal_folder,f'{prefix}_SB_p2_gain_phase_vs_time.png'))

""" Apply the solutions """
applycal(vis=SB_cont_p1+'.ms',spw=SB_contspws,
         spwmap=SB_spw_mapping, gaintable=[SB_p2], interp='linearPD',
         calwt=True, applymode='calonly')

""" Split off a corrected MS """
SB_cont_p2 = SB_cont_p1.replace('p1','p2')
os.system('rm -rf %s.ms*' % SB_cont_p2)
split(vis=SB_cont_p1+'.ms',outputvis=SB_cont_p2+'.ms',datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=SB_cont_p2+'.ms',imagename = SB_cont_p2,
               threshold = '0.78mJy', **SB_tclean_wrapper_kwargs)
estimate_SNR(SB_cont_p2+'.image', disk_mask = SB_mask,
             noise_mask = noise_annulus_SB)
generate_image_png(SB_cont_p2+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB,10*rms_SB],
                   save_folder=SB_selfcal_folder)
#HD_135344B_SB_contp2.image
#Beam 0.394 arcsec x 0.297 arcsec (-89.11 deg)
#Flux inside disk mask: 442.11 mJy
#Peak intensity of source: 66.63 mJy/beam
#rms: 1.07e-01 mJy/beam
#Peak SNR: 621.39


#Third round
SB_p3 = SB_p2.replace('p2','p3')
os.system('rm -rf '+SB_p3)
gaincal(vis=SB_cont_p2+'.ms', caltable=SB_p3,
        gaintype='T', spw=SB_contspws,refant=SB_refant, combine='spw,scan',
        calmode='p', solint='120s', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_p3,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_p3,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_selfcal_folder,f'{prefix}_SB_p3_gain_phase_vs_time.png')
       )

""" Apply the solutions """
applycal(vis=SB_cont_p2+'.ms', spw=SB_contspws,
         spwmap = SB_spw_mapping, gaintable=[SB_p3], interp='linearPD',
         calwt=True, applymode='calonly')

""" Split off a corrected MS """
SB_cont_p3 = SB_cont_p2.replace('p2','p3')
os.system('rm -rf %s.ms*' % SB_cont_p3)
split(vis=SB_cont_p2+'.ms',outputvis=SB_cont_p3+'.ms',datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=SB_cont_p3+'.ms',imagename = SB_cont_p3,
               threshold = '0.64mJy', **SB_tclean_wrapper_kwargs)
estimate_SNR(SB_cont_p3+'.image', disk_mask = SB_mask,
             noise_mask = noise_annulus_SB)
generate_image_png(SB_cont_p3+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB,10*rms_SB],
                   save_folder=SB_selfcal_folder)
#HD_135344B_SB_contp3.image
#Beam 0.394 arcsec x 0.297 arcsec (-89.11 deg)
#Flux inside disk mask: 442.18 mJy
#Peak intensity of source: 67.22 mJy/beam
#rms: 8.80e-02 mJy/beam
#Peak SNR: 764.00


#Fourth round
SB_p4 = SB_p3.replace('p3','p4')
os.system('rm -rf '+SB_p4)
gaincal(vis=SB_cont_p3+'.ms', caltable=SB_p4,
        gaintype='T', spw=SB_contspws,refant=SB_refant, combine='spw', calmode='p',
        solint='60s', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_p4,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_p4,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_selfcal_folder,f'{prefix}_SB_p4_gain_phase_vs_time.png')
       )

applycal(vis=SB_cont_p3+'.ms', spw=SB_contspws,
         spwmap = SB_spw_mapping, gaintable=[SB_p4], interp='linearPD',
         calwt=True, applymode='calonly')

""" Split off a corrected MS """
SB_cont_p4 = SB_cont_p3.replace('p3','p4')
os.system('rm -rf %s.ms*' % SB_cont_p4)
split(vis=SB_cont_p3+'.ms',outputvis=SB_cont_p4+'.ms',datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=SB_cont_p4+'.ms',imagename = SB_cont_p4,
               threshold = '0.64mJy',**SB_tclean_wrapper_kwargs)
estimate_SNR(SB_cont_p4+'.image', disk_mask = SB_mask,
             noise_mask = noise_annulus_SB)
generate_image_png(SB_cont_p4+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB,10*rms_SB],
                   save_folder=SB_selfcal_folder)
#HD_135344B_SB_contp4.image
#Beam 0.394 arcsec x 0.297 arcsec (-89.11 deg)
#Flux inside disk mask: 442.34 mJy
#Peak intensity of source: 67.51 mJy/beam
#rms: 8.99e-02 mJy/beam
#Peak SNR: 751.17


#Fifth round
SB_p5 = SB_p4.replace('p4','p5')
os.system('rm -rf '+SB_p5)
gaincal(vis=SB_cont_p4+'.ms', caltable=SB_p5,
        gaintype='T', spw=SB_contspws,refant=SB_refant, combine='spw', calmode='p',
        solint='20s', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_p5,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_p5,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_selfcal_folder,f'{prefix}_SB_p5_gain_phase_vs_time.png')
       )

applycal(vis=SB_cont_p4+'.ms', spw=SB_contspws,
         spwmap = SB_spw_mapping, gaintable=[SB_p5], interp='linearPD',
         calwt=True, applymode='calonly')

""" Split off a corrected MS """
SB_cont_p5 = SB_cont_p4.replace('p4','p5')
os.system('rm -rf %s.ms*' % SB_cont_p5)
split(vis=SB_cont_p4+'.ms',outputvis=SB_cont_p5+'.ms',datacolumn='corrected')


""" Image the results; check the resulting map """
tclean_wrapper(vis=SB_cont_p5+'.ms',imagename = SB_cont_p5,
               threshold = '0.64mJy',**SB_tclean_wrapper_kwargs)
estimate_SNR(SB_cont_p5+'.image', disk_mask = SB_mask,
             noise_mask = noise_annulus_SB)
generate_image_png(SB_cont_p5+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB,10*rms_SB],
                   save_folder=SB_selfcal_folder)
#HD_135344B_SB_contp5.image
#Beam 0.394 arcsec x 0.297 arcsec (-89.11 deg)
#Flux inside disk mask: 442.64 mJy
#Peak intensity of source: 67.88 mJy/beam
#rms: 9.19e-02 mJy/beam
#Peak SNR: 738.25

# from 120s, self-cal increases snr... let's see how to proceed now

#Check how SB selfcal improved things
#we do the check for each step of the self-cal to see how things improve at each step
non_self_caled_SB_vis = SB_cont_p0
self_caled_SB_visibilities = {'p1':SB_cont_p1,
                              'p2':SB_cont_p2,
                              'p3':SB_cont_p3,
                              'p4':SB_cont_p4,
                              'p5':SB_cont_p5}
    

SB_EBs = ('EB0','EB1')
SB_EB_spws = ('0,1,2,3','4,5,6,7')

for self_cal_step,self_caled_vis in self_caled_SB_visibilities.items():
    for EB_key,spw in zip(SB_EBs,SB_EB_spws):
        nametemplate = f'{prefix}_SB_{EB_key}_{self_cal_step}_compare_amp_vs_time'
        visibilities = [self_caled_vis+'.ms',non_self_caled_SB_vis+'.ms']
        plot_amp_vs_time_comparison(
                nametemplate=nametemplate,visibilities=visibilities,spw=spw,
                uvrange=uv_ranges['SB'],output_folder=SB_selfcal_folder)


all_SB_visibilities = self_caled_SB_visibilities.copy()
all_SB_visibilities['p0'] = SB_cont_p0

for self_cal_step,vis_name in all_SB_visibilities.items():
    #split out SB EBs
    vis_ms = vis_name+'.ms'
    nametemplate = vis_ms.replace('.ms','_EB')
    split_all_obs(msfile=vis_ms,nametemplate=nametemplate)
    exported_ms = []
    for i in range(number_of_EBs['SB']):
        EB_vis = f'{nametemplate}{i}.ms'
        export_MS(EB_vis) #export MS contents into Numpy save files
        exported_ms.append(EB_vis.replace('.ms','.vis.npz'))
    for i,exp_ms in enumerate(exported_ms):
        png_filename = f'flux_comparison_SB_EB{i}_{self_cal_step}_to_{flux_ref_EB}.png'
        plot_label = os.path.join(SB_selfcal_folder,png_filename)
        estimate_flux_scale(reference=f'{prefix}_{flux_ref_EB}_initcont_shift.vis.npz',
                            comparison=exp_ms,incl=incl,PA=PA,plot_label=plot_label)
    fluxscale = [1.,]*number_of_EBs['SB']
    plot_label = os.path.join(SB_selfcal_folder,
                              f'deprojected_vis_profiles_SB_{self_cal_step}.png')
    plot_deprojected(filelist=exported_ms,fluxscale=fluxscale, PA=PA, incl=incl,
                     show_err=True,plot_label=plot_label)


#The ratio of the fluxes of HD_135344B_SB_contp5_EB0.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 1.10293
#The scaling factor for gencal is 1.050 for your comparison measurement
#The error on the weighted mean ratio is 5.225e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_SB_contp5_EB1.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 0.98047
#The scaling factor for gencal is 0.990 for your comparison measurement
#The error on the weighted mean ratio is 4.676e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor


#self-cal removed the decoherence
#However, flux scaling is larger than 4% for EB1, so we need to do the scaling
#and repeat the SB self-cal
#If flux scaling is smaller than 4%, this would not be necessary

############ END of SB self-cal ############

############ BEGIN of SB self-cal 2 ############
#this is only necessary because we decided not to flux scale because of decoherence, and
#instead did SB self-cal; since there is still a flux offset >4% after SB self-cal,
#we need to scale and repeat
#If you scaled already in the first place, or if you did not scale and after SB self-cal
#the flux offsets are <4%, you don't ned to do this and you can skip the
#entire "SB self-cal 2" part of the script

#reminder: clean down to 6 sigma at each step

SB_scaled_selfcal_folder = get_figures_folderpath('7.1_selfcal_scaled_SB_figures')
make_figures_folder(SB_scaled_selfcal_folder)

rescale_flux(vis=prefix+'_SB_EB0_initcont_shift.ms', gencalparameter=[1.050])
#Splitting out rescaled values into new MS: HD_135344B_SB_EB0_initcont_shift_rescaled.ms

SB_scaled_cont_p0 = prefix+'_SB_scaled_contp0'
os.system('rm -rf %s.ms*' %SB_scaled_cont_p0)

concat(vis=[f'{prefix}_SB_EB0_initcont_shift_rescaled.ms',f'{prefix}_SB_EB1_initcont_shift.ms',],concatvis=SB_scaled_cont_p0+'.ms',
       dirtol='0.1arcsec',copypointing=False)

listobs(vis=SB_scaled_cont_p0+'.ms',listfile=SB_scaled_cont_p0+'.ms.txt',overwrite=True)

#go down to ~6 sigma
tclean_wrapper(vis=SB_scaled_cont_p0+'.ms',imagename = SB_scaled_cont_p0,
               threshold = '0.78mJy', **SB_tclean_wrapper_kwargs)
estimate_SNR(SB_scaled_cont_p0+'.image', disk_mask = SB_mask,noise_mask = noise_annulus_SB)
#HD_135344B_SB_scaled_contp0.image
#Beam 0.388 arcsec x 0.291 arcsec (-88.48 deg)
#Flux inside disk mask: 424.22 mJy
#Peak intensity of source: 61.52 mJy/beam
#rms: 1.15e-01 mJy/beam
#Peak SNR: 533.37

rms_SB_scaled = imstat(imagename = SB_scaled_cont_p0+'.image',region = noise_annulus_SB)['rms'][0]
generate_image_png(SB_scaled_cont_p0+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB_scaled,10*rms_SB_scaled],
                   save_folder=SB_scaled_selfcal_folder)


#First round
SB_scaled_p1 = prefix+'_SB_scaled_p1'
os.system('rm -rf '+SB_scaled_p1)
gaincal(vis=SB_scaled_cont_p0+'.ms',caltable=SB_scaled_p1,
        gaintype='G', spw=SB_contspws,refant=SB_refant, combine='scan,spw',
        calmode='p', solint='inf', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_scaled_p1,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_scaled_p1,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_scaled_selfcal_folder,
                             f'{prefix}_SB_p1_gain_phase_vs_time.png')
       )

""" Apply the solutions """
applycal(vis=SB_scaled_cont_p0+'.ms',spw=SB_contspws,
         spwmap=SB_spw_mapping,gaintable=[SB_scaled_p1], interp='linearPD',
         calwt=True, applymode='calonly')

SB_scaled_cont_p1 = SB_scaled_cont_p0.replace('p0','p1')
os.system('rm -rf %s.ms*' % SB_scaled_cont_p1)
split(vis=SB_scaled_cont_p0+'.ms',outputvis=SB_scaled_cont_p1+'.ms', datacolumn='corrected')

#again threshold should be ~6sigma
tclean_wrapper(vis=SB_scaled_cont_p1+'.ms',imagename = SB_scaled_cont_p1,
               threshold = '0.78mJy', **SB_tclean_wrapper_kwargs)
estimate_SNR(SB_scaled_cont_p1+'.image',disk_mask=SB_mask,noise_mask=noise_annulus_SB)
generate_image_png(SB_scaled_cont_p1+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB_scaled,10*rms_SB_scaled],
                   save_folder=SB_scaled_selfcal_folder)
#HD_135344B_SB_scaled_contp1.image
#Beam 0.388 arcsec x 0.291 arcsec (-88.48 deg)
#Flux inside disk mask: 424.17 mJy
#Peak intensity of source: 61.50 mJy/beam
#rms: 1.13e-01 mJy/beam
#Peak SNR: 545.37


#Second round
SB_scaled_p2 = SB_scaled_p1.replace('p1','p2')
os.system('rm -rf '+SB_scaled_p2)
gaincal(vis=SB_scaled_cont_p1+'.ms',caltable=SB_scaled_p2,
        gaintype='T',spw=SB_contspws,refant=SB_refant, combine='scan,spw',
        calmode='p', solint='360s', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_scaled_p2,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_scaled_p2,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_scaled_selfcal_folder,f'{prefix}_SB_p2_gain_phase_vs_time.png'))

""" Apply the solutions """
applycal(vis=SB_scaled_cont_p1+'.ms',spw=SB_contspws,
         spwmap=SB_spw_mapping, gaintable=[SB_scaled_p2], interp='linearPD',
         calwt=True, applymode='calonly')

""" Split off a corrected MS """
SB_scaled_cont_p2 = SB_scaled_cont_p1.replace('p1','p2')
os.system('rm -rf %s.ms*' % SB_scaled_cont_p2)
split(vis=SB_scaled_cont_p1+'.ms',outputvis=SB_scaled_cont_p2+'.ms',datacolumn='corrected')


""" Image the results; check the resulting map """
tclean_wrapper(vis=SB_scaled_cont_p2+'.ms',imagename = SB_scaled_cont_p2,
               threshold = '0.78mJy', **SB_tclean_wrapper_kwargs)
estimate_SNR(SB_scaled_cont_p2+'.image', disk_mask = SB_mask,
             noise_mask = noise_annulus_SB)
generate_image_png(SB_scaled_cont_p2+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB_scaled,10*rms_SB_scaled],
                   save_folder=SB_scaled_selfcal_folder)
#HD_135344B_SB_scaled_contp2.image
#Beam 0.388 arcsec x 0.291 arcsec (-88.48 deg)
#Flux inside disk mask: 424.73 mJy
#Peak intensity of source: 62.02 mJy/beam
#rms: 8.80e-02 mJy/beam
#Peak SNR: 704.64


#Third round
SB_scaled_p3 = SB_scaled_p2.replace('p2','p3')
os.system('rm -rf '+SB_scaled_p3)
gaincal(vis=SB_scaled_cont_p2+'.ms', caltable=SB_scaled_p3,
        gaintype='T', spw=SB_contspws,refant=SB_refant, combine='spw',
        calmode='p', solint='120s', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_scaled_p3,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_scaled_p3,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_scaled_selfcal_folder,f'{prefix}_SB_p3_gain_phase_vs_time.png')
       )

""" Apply the solutions """
applycal(vis=SB_scaled_cont_p2+'.ms', spw=SB_contspws,
         spwmap = SB_spw_mapping, gaintable=[SB_scaled_p3], interp='linearPD',
         calwt=True, applymode='calonly')

""" Split off a corrected MS """
SB_scaled_cont_p3 = SB_scaled_cont_p2.replace('p2','p3')
os.system('rm -rf %s.ms*' % SB_scaled_cont_p3)
split(vis=SB_scaled_cont_p2+'.ms',outputvis=SB_scaled_cont_p3+'.ms',datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=SB_scaled_cont_p3+'.ms',imagename = SB_scaled_cont_p3,
               threshold = '0.64mJy', **SB_tclean_wrapper_kwargs)
estimate_SNR(SB_scaled_cont_p3+'.image', disk_mask = SB_mask,
             noise_mask = noise_annulus_SB)
generate_image_png(SB_scaled_cont_p3+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB_scaled,10*rms_SB_scaled],
                   save_folder=SB_scaled_selfcal_folder)
#HD_135344B_SB_scaled_contp3.image
#Beam 0.388 arcsec x 0.291 arcsec (-88.48 deg)
#Flux inside disk mask: 424.78 mJy
#Peak intensity of source: 62.61 mJy/beam
#rms: 6.22e-02 mJy/beam
#Peak SNR: 1006.30


#Fourth round
SB_scaled_p4 = SB_scaled_p3.replace('p3','p4')
os.system('rm -rf '+SB_scaled_p4)
gaincal(vis=SB_scaled_cont_p3+'.ms', caltable=SB_scaled_p4,
        gaintype='T', spw=SB_contspws,refant=SB_refant, combine='spw', calmode='p',
        solint='60s', minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(SB_scaled_p4,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(SB_scaled_p4,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(SB_scaled_selfcal_folder,f'{prefix}_SB_p4_gain_phase_vs_time.png')
       )

applycal(vis=SB_scaled_cont_p3+'.ms', spw=SB_contspws,
         spwmap = SB_spw_mapping, gaintable=[SB_scaled_p4], interp='linearPD',
         calwt=True, applymode='calonly')

""" Split off a corrected MS """
SB_scaled_cont_p4 = SB_scaled_cont_p3.replace('p3','p4')
os.system('rm -rf %s.ms*' % SB_scaled_cont_p4)
split(vis=SB_scaled_cont_p3+'.ms',outputvis=SB_scaled_cont_p4+'.ms',datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=SB_scaled_cont_p4+'.ms',imagename = SB_scaled_cont_p4,
               threshold = '0.64mJy',**SB_tclean_wrapper_kwargs)
estimate_SNR(SB_scaled_cont_p4+'.image', disk_mask = SB_mask,
             noise_mask = noise_annulus_SB)
generate_image_png(SB_scaled_cont_p4+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_SB_scaled,10*rms_SB_scaled],
                   save_folder=SB_scaled_selfcal_folder)
#HD_135344B_SB_scaled_contp4.image
#Beam 0.388 arcsec x 0.291 arcsec (-88.48 deg)
#Flux inside disk mask: 425.00 mJy
#Peak intensity of source: 62.87 mJy/beam
#rms: 6.27e-02 mJy/beam
#Peak SNR: 1002.23

#We stop at 60s without going to 20s because rms increases, and de-coherence is not particuarly strong

#Check again how SB selfcal improved things
#we do the check for each step of the self-cal to see how things improve at each step

non_self_caled_scaled_SB_vis = SB_scaled_cont_p0
self_caled_scaled_SB_visibilities = {'p1':SB_scaled_cont_p1,
                                     'p2':SB_scaled_cont_p2,
                                     'p3':SB_scaled_cont_p3,
                                     'p4':SB_scaled_cont_p4}

SB_EBs = ('EB0','EB1')
SB_EB_spws = ('0,1,2,3','4,5,6,7')

for self_cal_step,self_caled_vis in self_caled_scaled_SB_visibilities.items():
    for EB_key,spw in zip(SB_EBs,SB_EB_spws):
        nametemplate = f'{prefix}_SB_scaled_{EB_key}_{self_cal_step}_compare'\
                        +'_amp_vs_time'
        visibilities=[self_caled_vis+'.ms',non_self_caled_scaled_SB_vis+'.ms']
        plot_amp_vs_time_comparison(
                nametemplate=nametemplate,visibilities=visibilities,spw=spw,
                uvrange=uv_ranges['SB'],output_folder=SB_scaled_selfcal_folder)


all_scaled_SB_visibilities = self_caled_scaled_SB_visibilities.copy()
all_scaled_SB_visibilities['p0'] = SB_scaled_cont_p0

for self_cal_step,vis_name in all_scaled_SB_visibilities.items():
    #split out SB EBs
    vis_ms = vis_name+'.ms'
    nametemplate = vis_ms.replace('.ms','_EB')
    split_all_obs(msfile=vis_ms,nametemplate=nametemplate)
    exported_ms = []
    for i in range(number_of_EBs['SB']):
        EB_vis = f'{nametemplate}{i}.ms'
        export_MS(EB_vis) #export MS contents into Numpy save files
        exported_ms.append(EB_vis.replace('.ms','.vis.npz'))
    for i,exp_ms in enumerate(exported_ms):
        png_filename = f'scaled_flux_comparison_SB_EB{i}_{self_cal_step}'\
                       +f'_to_{flux_ref_EB}.png'
        plot_label = os.path.join(SB_scaled_selfcal_folder,png_filename)
        estimate_flux_scale(reference=f'{prefix}_{flux_ref_EB}_initcont_shift.vis.npz',
                            comparison=exp_ms,incl=incl,PA=PA,plot_label=plot_label)
    fluxscale = [1.,]*number_of_EBs['SB']
    plot_label = os.path.join(SB_scaled_selfcal_folder,
                              f'deprojected_vis_profiles_scaled_SB_{self_cal_step}.png')
    plot_deprojected(filelist=exported_ms,fluxscale=fluxscale, PA=PA, incl=incl,
                     show_err=True,plot_label=plot_label)

#The ratio of the fluxes of HD_135344B_SB_scaled_contp4_EB0.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 0.99533
#The scaling factor for gencal is 0.998 for your comparison measurement
#The error on the weighted mean ratio is 4.719e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#The ratio of the fluxes of HD_135344B_SB_scaled_contp4_EB1.vis.npz to
#HD_135344B_LB_EB0_initcont_shift.vis.npz is 0.97871
#The scaling factor for gencal is 0.989 for your comparison measurement
#The error on the weighted mean ratio is 4.669e-04, although it's likely that
#the weights in the measurement sets are too off by some constant factor

#It worked, scaling is now below 4%

############ END of SB self-cal 2 ############

"""SELF-CAL COMBINED DATA"""
#phase cal down to 6 sigma, amp cal down to 1 sigma

LB_selfcal_folder = get_figures_folderpath('8_selfcal_SBLB_figures')
make_figures_folder(LB_selfcal_folder)

""" Merge the SB self-cal'ed ms with LB ms"""
LB_cont_p0 = prefix+'_SBLB_contp0'
os.system('rm -rf %s.ms*' % LB_cont_p0)

concat(vis=[SB_scaled_cont_p4+'.ms',
            f'{prefix}_LB_EB0_initcont_shift.ms',
            f'{prefix}_LB_EB1_initcont_shift_rescaled.ms',
            f'{prefix}_LB_EB2_initcont_shift_rescaled.ms',
            f'{prefix}_LB_EB3_initcont_shift.ms'],
            concatvis=LB_cont_p0+'.ms',dirtol='0.1arcsec',copypointing=False)
#I got a warning about possibility of duplicate scan numbers, but looking at the
#listobs output, everything seems ok

listobs(vis=LB_cont_p0+'.ms',listfile=LB_cont_p0+'.ms.txt',overwrite=True)

mask_ra = '15h15m48.412300s'
mask_dec = '-37.09.16.53940'

LB_mask = f'ellipse[[{mask_ra},{mask_dec}], [{mask_semimajor:.3f}arcsec,'\
         +f' {mask_semiminor:.3f}arcsec], {mask_pa:.1f}deg]'
noise_annulus_LB = f"annulus[[{mask_ra}, {mask_dec}],['4.arcsec', '6.arcsec']]"

LB_tclean_wrapper_kwargs = {'mask':LB_mask,'deconvolver':'multiscale',
                            'scales':scales['LB'],'savemodel':'modelcolumn',
                            'imsize':imsize['LB'],'cellsize':cellsize['LB'],
                            'robust':0.5,'interactive':False,
                            'parallel':use_parallel,'gridder':'standard'}


""" clean down to ~6 sigma"""
tclean_wrapper(vis=LB_cont_p0+'.ms', imagename = LB_cont_p0,
               threshold = '0.22mJy',**LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_p0+'.image', disk_mask=LB_mask, noise_mask=noise_annulus_LB)
rms_LB = imstat(imagename = LB_cont_p0+'.image', region = noise_annulus_LB)['rms'][0]
generate_image_png(LB_cont_p0+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contp0.image
#Beam 0.163 arcsec x 0.129 arcsec (-77.91 deg)
#Flux inside disk mask: 423.97 mJy
#Peak intensity of source: 16.21 mJy/beam
#rms: 3.92e-02 mJy/beam
#Peak SNR: 413.84


""" Look for references antennas from weblog, and pick the first that are listed, overlapping with all EBs """
""" Since we are combined SB EBs to LB EBs, ref antennas for both SB and LB are needed """
# For LBs:
# DA55, DV04, DV25

# For the SBs, we had: SB_refant   = 'DA63@A035, DA57@A001'

for ref_ant in ('DA55','DV04','DV25','DA63','DA57'):
    get_station_numbers(LB_cont_p0+'.ms',ref_ant)
#Observation ID 0: DA55@A043
#Observation ID 1: DA55@A043
#Observation ID 2: DA55@A043
#Observation ID 3: DA55@A043
#Observation ID 4: DA55@A043
#Observation ID 5: DA55@A043
#Observation ID 0: DV04@A007
#Observation ID 2: DV04@A007
#Observation ID 3: DV04@A007
#Observation ID 4: DV04@A007
#Observation ID 5: DV04@A007
#Observation ID 0: DV25@A011
#Observation ID 1: DV25@A011
#Observation ID 2: DV25@A011
#Observation ID 3: DV25@A011
#Observation ID 4: DV25@A011
#Observation ID 5: DV25@A011
#Observation ID 0: DA63@A035
#Observation ID 1: DA63@A035
#Observation ID 2: DA63@A116
#Observation ID 3: DA63@A116
#Observation ID 4: DA63@A116
#Observation ID 5: DA63@A116
#Observation ID 0: DA57@A001
#Observation ID 1: DA57@A001
#Observation ID 2: DA57@A104
#Observation ID 3: DA57@A104
#Observation ID 4: DA57@A104
#Observation ID 5: DA57@A104

""" Self-calibration parameters """
LB_contspws = '0~23'
LB_refant   = 'DA63@A035, DA57@A001, DA55@A043, DV04@A007'

LB_spw_mapping = [0,0,0,0,4,4,4,4,8,8,8,8,12,12,12,12,16,16,16,16,20,20,20,20]

LB_p1 = prefix+'_SBLB.p1'
os.system('rm -rf '+LB_p1)
#if you get many flagged solutions, change gaintype to 'T'
gaincal(vis=LB_cont_p0+'.ms', caltable=LB_p1, gaintype='G', spw=LB_contspws,
        refant=LB_refant, combine='scan,spw', calmode='p', solint='inf',
        minsnr=3., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(LB_p1,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(LB_p1,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_p1_gain_phase_vs_time.png'))

""" Apply the solutions """
applycal(vis=LB_cont_p0+'.ms', spw=LB_contspws, spwmap = LB_spw_mapping,
         gaintable=[LB_p1], interp='linearPD', calwt=True, applymode='calonly')

""" Split off a corrected MS """
LB_cont_p1 = prefix+'_SBLB_contp1'
os.system('rm -rf %s.ms*' % LB_cont_p1)
split(vis=LB_cont_p0+'.ms', outputvis=LB_cont_p1+'.ms', datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=LB_cont_p1+'.ms',imagename=LB_cont_p1,threshold='0.22mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_p1+'.image', disk_mask=LB_mask, noise_mask=noise_annulus_LB)
generate_image_png(LB_cont_p1+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contp1.image
#Beam 0.163 arcsec x 0.129 arcsec (-77.91 deg)
#Flux inside disk mask: 424.10 mJy
#Peak intensity of source: 16.16 mJy/beam
#rms: 3.80e-02 mJy/beam
#Peak SNR: 425.75


""" Second round of phase-only self-cal """
LB_p2 = prefix+'_SBLB.p2'
os.system('rm -rf '+LB_p2)
#solint='360s' resulted in "mismatched frequencies" error, so I slighlty changed it
gaincal(vis=LB_cont_p1+'.ms', caltable=LB_p2, gaintype='T', spw=LB_contspws,
        refant=LB_refant, combine='spw,scan', calmode='p', solint='360s',
        minsnr=2., minblperant=4)

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(LB_p2,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(LB_p2,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_p2_gain_phase_vs_time.png'))

""" Apply the solutions """
applycal(vis=LB_cont_p1+'.ms', spw=LB_contspws, spwmap = LB_spw_mapping,
         gaintable=[LB_p2], interp='linearPD', calwt=True, applymode='calonly')

""" Split off a corrected MS """
LB_cont_p2 = prefix+'_SBLB_contp2'
os.system('rm -rf %s.ms*' % LB_cont_p2)
split(vis=LB_cont_p1+'.ms', outputvis=LB_cont_p2+'.ms', datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=LB_cont_p2+'.ms', imagename = LB_cont_p2, threshold = '0.17mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_p2+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(LB_cont_p2+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contp2.image
#Beam 0.163 arcsec x 0.129 arcsec (-77.91 deg)
#Flux inside disk mask: 423.64 mJy
#Peak intensity of source: 16.39 mJy/beam
#rms: 2.81e-02 mJy/beam
#Peak SNR: 584.18


""" Third round of phase-only self-cal """
LB_p3 = prefix+'_SBLB.p3'
os.system('rm -rf '+LB_p3)
gaincal(vis=LB_cont_p2+'.ms', caltable=LB_p3, gaintype='T', spw=LB_contspws,
        refant=LB_refant, combine='spw', calmode='p', solint='120s',
        minsnr=2., minblperant=4)
#minor flagging, up to 4/40 antennas flagged in LB data

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(LB_p3,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(LB_p3,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_p3_gain_phase_vs_time.png'))

""" Apply the solutions """
applycal(vis=LB_cont_p2+'.ms', spw=LB_contspws, spwmap = LB_spw_mapping,
         gaintable=[LB_p3], interp='linearPD', calwt=True, applymode='calonly')

""" Split off a corrected MS """
LB_cont_p3 = prefix+'_SBLB_contp3'
os.system('rm -rf %s.ms*' % LB_cont_p3)
split(vis=LB_cont_p2+'.ms', outputvis=LB_cont_p3+'.ms', datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=LB_cont_p3+'.ms', imagename = LB_cont_p3, threshold = '0.17mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_p3+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(LB_cont_p3+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contp3.image
#Beam 0.163 arcsec x 0.129 arcsec (-77.91 deg)
#Flux inside disk mask: 423.63 mJy
#Peak intensity of source: 16.49 mJy/beam
#rms: 2.62e-02 mJy/beam
#Peak SNR: 628.64

""" Fourth round of phase-only self-cal """
LB_p4 = prefix+'_SBLB.p4'
os.system('rm -rf '+LB_p4)
gaincal(vis=LB_cont_p3+'.ms', caltable=LB_p4, gaintype='T', spw=LB_contspws,
        refant=LB_refant, combine='spw', calmode='p', solint='60s',
        minsnr=2., minblperant=4)
#minor flagging, up to 4/40 antennas flagged in LB data

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(LB_p4,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(LB_p4,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_p4_gain_phase_vs_time.png'))

""" Apply the solutions """
applycal(vis=LB_cont_p3+'.ms', spw=LB_contspws, spwmap = LB_spw_mapping,
         gaintable=[LB_p4], interp='linearPD', calwt=True, applymode='calonly')

""" Split off a corrected MS """
LB_cont_p4 = prefix+'_SBLB_contp4'
os.system('rm -rf %s.ms*' % LB_cont_p4)
split(vis=LB_cont_p3+'.ms', outputvis=LB_cont_p4+'.ms', datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=LB_cont_p4+'.ms', imagename = LB_cont_p4, threshold = '0.17mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_p4+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(LB_cont_p4+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contp4.image
#Beam 0.163 arcsec x 0.129 arcsec (-77.91 deg)
#Flux inside disk mask: 423.82 mJy
#Peak intensity of source: 16.55 mJy/beam
#rms: 2.58e-02 mJy/beam
#Peak SNR: 641.63

""" Fifth round of phase-only self-cal """
LB_p5 = prefix+'_SBLB.p5'
os.system('rm -rf '+LB_p5)
gaincal(vis=LB_cont_p4+'.ms', caltable=LB_p5, gaintype='T', spw=LB_contspws,
        refant=LB_refant, combine='spw', calmode='p', solint='30s',
        minsnr=2., minblperant=4)
#minor flagging, up to 5/40 antennas flagged in all LB data

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(LB_p5,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(LB_p5,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_p5_gain_phase_vs_time.png'))


applycal(vis=LB_cont_p4+'.ms', spw=LB_contspws, spwmap = LB_spw_mapping,
         gaintable=[LB_p5], interp='linearPD', calwt=True, applymode='calonly')

""" Split off a corrected MS """
LB_cont_p5 = prefix+'_SBLB_contp5'
os.system('rm -rf %s.ms*' % LB_cont_p5)
split(vis=LB_cont_p4+'.ms', outputvis=LB_cont_p5+'.ms', datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=LB_cont_p5+'.ms', imagename = LB_cont_p5, threshold = '0.17mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_p5+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(LB_cont_p5+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contp5.image
#Beam 0.163 arcsec x 0.129 arcsec (-77.91 deg)
#Flux inside disk mask: 423.91 mJy
#Peak intensity of source: 16.65 mJy/beam
#rms: 2.56e-02 mJy/beam
#Peak SNR: 650.88

""" Sixth round of phase-only self-cal """
LB_p6 = prefix+'_SBLB.p6'
os.system('rm -rf '+LB_p6)
gaincal(vis=LB_cont_p5+'.ms', caltable=LB_p6, gaintype='T', spw=LB_contspws,
        refant=LB_refant, combine='spw', calmode='p', solint='18s',
        minsnr=2., minblperant=4)
#minor flagging, up to 6/40 antennas flagged in all LB data

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(LB_p6,xaxis='time', yaxis='GainPhase',iteraxis='spw')
""" Print calibration png file """
plotms(LB_p6,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_p6_gain_phase_vs_time.png'))


applycal(vis=LB_cont_p5+'.ms', spw=LB_contspws, spwmap = LB_spw_mapping,
         gaintable=[LB_p6], interp='linearPD', calwt=True, applymode='calonly')

""" Split off a corrected MS """
LB_cont_p6 = prefix+'_SBLB_contp6'
os.system('rm -rf %s.ms*' % LB_cont_p6)
split(vis=LB_cont_p5+'.ms', outputvis=LB_cont_p6+'.ms', datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=LB_cont_p6+'.ms', imagename = LB_cont_p6, threshold = '0.17mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_p6+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(LB_cont_p6+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contp6.image
#Beam 0.163 arcsec x 0.129 arcsec (-77.91 deg)
#Flux inside disk mask: 424.12 mJy
#Peak intensity of source: 16.66 mJy/beam
#rms: 2.55e-02 mJy/beam
#Peak SNR: 652.22


""" Clean down to 1 sigma before amplitude self-cal"""

tclean_wrapper(vis=LB_cont_p6+'.ms', imagename = LB_cont_p6, threshold = '0.025mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_p6+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)

#HD_135344B_SBLB_contp6.image
#Beam 0.163 arcsec x 0.129 arcsec (-77.91 deg)
#Flux inside disk mask: 425.74 mJy
#Peak intensity of source: 16.72 mJy/beam
#rms: 2.45e-02 mJy/beam
#Peak SNR: 683.25


""" Amplitude self-cal"""
LB_ap0 = prefix+'_SBLB.ap0'
os.system('rm -rf '+LB_ap0)
gaincal(vis=LB_cont_p6+'.ms', caltable=LB_ap0, gaintype='T', spw=LB_contspws,
        refant=LB_refant, combine='spw, scan', calmode='ap', solint='inf', minsnr=5.0,
        minblperant=4, solnorm=False)
# no flagging, but a few solutions manually flagged in LBs

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(LB_ap0,xaxis='time', yaxis='GainPhase',iteraxis='spw')
plotms(LB_ap0,xaxis='time', yaxis='GainAmp',iteraxis='spw')

""" Print calibration png file """
plotms(LB_ap0,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_ap0_gain_phase_vs_time.png'))
plotms(LB_ap0,xaxis='time', yaxis='GainAmp',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_ap0_gain_amp_vs_time.png'))

""" Apply the solutions """
applycal(vis=LB_cont_p6+'.ms', spw=LB_contspws, spwmap = LB_spw_mapping,
         gaintable=[LB_ap0], interp='linearPD', calwt=True, applymode='calonly')

""" Split off a corrected MS """
LB_cont_ap0 = prefix+'_SBLB_contap0'
os.system('rm -rf %s.ms*' % LB_cont_ap0)
split(vis=LB_cont_p6+'.ms', outputvis=LB_cont_ap0+'.ms', datacolumn='corrected')

""" Image the results; check the resulting map """
#clean again down to 1 sigma
tclean_wrapper(vis=LB_cont_ap0+'.ms', imagename = LB_cont_ap0, threshold = '0.025mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_ap0+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(LB_cont_ap0+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contap0.image
#Beam 0.164 arcsec x 0.130 arcsec (-77.49 deg)
#Flux inside disk mask: 426.76 mJy
#Peak intensity of source: 16.73 mJy/beam
#rms: 2.37e-02 mJy/beam
#Peak SNR: 706.53

""" Try ampl self-cal on SB scan length intervals (~360s)"""
LB_ap1 = prefix+'_SBLB.ap1'
os.system('rm -rf '+LB_ap1)
gaincal(vis=LB_cont_ap0+'.ms', caltable=LB_ap1, gaintype='T', spw=LB_contspws,
        refant=LB_refant, combine='spw,scan', calmode='ap', solint='360s', minsnr=5.0,
        minblperant=4, solnorm=False)
#minor flagging, up to 4/40 antennas flagged in all LB data

""" Inspect gain tables interactively and decide whether to manually flag something"""
plotms(LB_ap1,xaxis='time', yaxis='GainPhase',iteraxis='spw')
plotms(LB_ap1,xaxis='time', yaxis='GainAmp',iteraxis='spw')

""" Print calibration png file """
plotms(LB_ap1,xaxis='time', yaxis='GainPhase',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_LB_ap1_gain_phase_vs_time.png'))
plotms(LB_ap1,xaxis='time', yaxis='GainAmp',iteraxis='spw',exprange='all',
       overwrite=True,showgui=False,
       plotfile=os.path.join(LB_selfcal_folder,f'{prefix}_ap1_LB_gain_amp_vs_time.png'))

""" Apply the solutions """
applycal(vis=LB_cont_ap0+'.ms', spw=LB_contspws, spwmap = LB_spw_mapping,
         gaintable=[LB_ap1], interp='linearPD', calwt=True, applymode='calonly')

""" Split off a corrected MS """
LB_cont_ap1 = prefix+'_SBLB_contap1'
os.system('rm -rf %s.ms*' % LB_cont_ap1)
split(vis=LB_cont_ap0+'.ms', outputvis=LB_cont_ap1+'.ms', datacolumn='corrected')

""" Image the results; check the resulting map """
tclean_wrapper(vis=LB_cont_ap1+'.ms', imagename = LB_cont_ap1,threshold = '0.025mJy',
               **LB_tclean_wrapper_kwargs)
estimate_SNR(LB_cont_ap1+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(LB_cont_ap1+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],
                   save_folder=LB_selfcal_folder)
#HD_135344B_SBLB_contap1.image
#Beam 0.163 arcsec x 0.130 arcsec (-77.52 deg)
#Flux inside disk mask: 426.93 mJy
#Peak intensity of source: 16.58 mJy/beam
#rms: 2.33e-02 mJy/beam
#Peak SNR: 712.63

#only minor increase of SNR, but images look fine

#Now check the flux scaling

self_caled_LB_visibilities = {'p1':LB_cont_p1,
                              'p2':LB_cont_p2,
                              'p3':LB_cont_p3,
                              'p4':LB_cont_p4,
                              'p5':LB_cont_p5,
                              'p6':LB_cont_p6,
                              'ap0':LB_cont_ap0,
                              'ap1':LB_cont_ap1}

for vis in self_caled_LB_visibilities.values(): 
    listobs(vis=vis,listfile=vis+'.ms.txt',overwrite=True)

LB_EBs = ('EB2','EB3','EB4','EB5')
LB_EB_spws = ('8,9,10,11','12,13,14,15','16,17,18,19','20,21,22,23') #fill out by referring to listobs output

for self_cal_step,self_caled_vis in self_caled_LB_visibilities.items():
    for EB_key,spw in zip(LB_EBs,LB_EB_spws):
        nametemplate = f'{prefix}_LB_{EB_key}_{self_cal_step}_compare_amp_vs_time'
        visibilities = [self_caled_vis+'.ms',LB_cont_p0+'.ms']
        plot_amp_vs_time_comparison(
                nametemplate=nametemplate,visibilities=visibilities,spw=spw,
                uvrange=uv_ranges['LB'],output_folder=LB_selfcal_folder)


#set to the EB of the combined SBLB data that corresponds to flux_ref_EB
SBLB_flux_ref_EB = 2 #this is LB EB0

total_number_of_EBs = number_of_EBs['SB'] + number_of_EBs['LB']
for self_cal_step,vis in self_caled_LB_visibilities.items():
    nametemplate = f'{prefix}_SBLB_cont{self_cal_step}_EB'
    split_all_obs(msfile=vis+'.ms',nametemplate=nametemplate)
    for i in range(total_number_of_EBs):
        export_MS(f'{nametemplate}{i}.ms')
    for i in range(total_number_of_EBs):
        reference = f'{nametemplate}{SBLB_flux_ref_EB}.vis.npz'
        output = f'flux_comparison_EB{i}_to_EB{SBLB_flux_ref_EB}'\
                       +f'_SBLB_{self_cal_step}.png'
        plot_label = os.path.join(LB_selfcal_folder,output)
        estimate_flux_scale(reference=reference,
                            comparison=f'{nametemplate}{i}.vis.npz',
                            incl=incl, PA=PA,uvbins = np.arange(40.,300.,20.),
                            plot_label=plot_label)
    filelist = [f'{nametemplate}{i}.vis.npz' for i in range(total_number_of_EBs)]
    fluxscale = [1.,]*total_number_of_EBs
    plot_label = os.path.join(LB_selfcal_folder,
                              f'deprojected_vis_profiles_SBLB_{self_cal_step}.png')
    plot_deprojected(filelist=filelist,fluxscale=fluxscale, PA=PA, incl=incl,
                     show_err=True,plot_label=plot_label)


""" Split out final continuum ms table, with a 30s timebin
"""
#comparing ap0 and ap1, the SNR is almost the same, and the flux scaling is fine for both
#however, ap1 seems to have a slightly "better" noise structure when looking at the
#images. So I choose ap1, although there was some flagging (~10%), so this choice
#should be further discussed

LB_cont_averaged = f'{prefix}_time_ave_continuum'
os.system(f'rm -rf {LB_cont_averaged}.ms*')
split(vis=LB_cont_ap1+'.ms', outputvis=LB_cont_averaged+'.ms', datacolumn='data',
      keepflags=False, timebin='30s')


"""
Now apply these solutions to the line data
"""

calibrate_linedata_folder = get_figures_folderpath('9_apply_cal_to_lines')
make_figures_folder(calibrate_linedata_folder)

""" Check that lines are not flagged in not averaged data"""
for params in data_params.values():
    plotfile = os.path.join(
                calibrate_linedata_folder,
                f'{prefix}_{params["name"]}_chan-v-amp_preselfcal_after_flagging.png')
    plotms(vis=params['vis'],
           xaxis='channel',
           yaxis='amplitude',
           field=params['field'],
           ydatacolumn='data',
           avgtime='1e8',
           avgscan=True,
           avgbaseline=True,
           coloraxis='corr',
           iteraxis='spw',
           showgui = False,
           exprange='all',
           plotfile=plotfile)


""" Apply gaintables of individual EBs"""
for params in data_params.values():
    single_EB_p1 = f'{prefix}_{params["name"]}_initcont.p1'
    vis = f'{prefix}_{params["name"]}.ms'
    applycal(vis=vis,spw='0~3',spwmap=[0,0,0,0],gaintable=[single_EB_p1],
             interp='linearPD',applymode='calonly',calwt=True)
    split(vis=vis,outputvis=vis[:-3]+'_no_ave_selfcal.ms',datacolumn='corrected')

### ALIGN DATA ###
# we re-align the no_ave data, as we have done for the "initcont" ms tables.
# We go from *_no_ave_selfcal.ms to *_no_ave_shift.ms

reference_ms = {'LB':reference_for_LB_alignment,
                'SB':reference_for_SB_alignment}
for params in data_params.values():
    unshifted_ms = f'{prefix}_{params["name"]}_no_ave_selfcal.ms'
    array_key,_ = params['name'].split('_') #LB or SB
    offset = alignment_offsets[params['name']]
    #npix and cell_size are not needed because we do not fit any offset
    alignment.align_measurement_sets(
            reference_ms=reference_ms[array_key],align_ms=[unshifted_ms],
            align_offsets=[offset],npix=None,cell_size=None)

### END OF ALIGN DATA ###


"""
If you have re-scaled fluxes, you need to re-scale the shifted *no_ave* EBs as well
"""
rescale_flux(vis=prefix+'_SB_EB0_no_ave_selfcal_shift.ms', gencalparameter=[1.050])
rescale_flux(vis=prefix+'_LB_EB1_no_ave_selfcal_shift.ms', gencalparameter=[1.020])
rescale_flux(vis=prefix+'_LB_EB2_no_ave_selfcal_shift.ms', gencalparameter=[0.969])


""" Concat not averaged SB data """
SB_combined = f'{prefix}_SB_no_ave_concat'
os.system('rm -rf %s.ms*' % SB_combined)
concat(vis=[f'{prefix}_SB_EB0_no_ave_selfcal_shift_rescaled.ms',
            f'{prefix}_SB_EB1_no_ave_selfcal_shift.ms'],
       concatvis=SB_combined+'.ms', dirtol='0.1arcsec', copypointing=False)

listobs(vis=SB_combined+'.ms',listfile=SB_combined+'.ms.txt',overwrite=True)

#BE CAREFUL HERE
#since I did the SB self-cal twice (because there was decoherence), I need to use
#the gaintables from the second SB self-cal here
#If you did not do that, then obviously you need to use SB_p1, SB_p2,...
applycal(vis=SB_combined+'.ms', spw='0~7',
         gaintable=[SB_scaled_p1,SB_scaled_p2,SB_scaled_p3,SB_scaled_p4],
         spwmap = [SB_spw_mapping]*4,interp=['linearPD']*4, calwt=True,
         applymode='calonly',flagbackup=False)

SB_no_ave_selfcal = f'{prefix}_SB_no_ave_selfcal.ms'
os.system(f'rm -rf {SB_no_ave_selfcal}*')
split(vis=SB_combined+'.ms', outputvis=SB_no_ave_selfcal,datacolumn='corrected')

""" Concat not averaged LB data """

LB_combined = f'{prefix}_SBLB_no_ave_concat.ms'
os.system(f'rm -rf {LB_combined}*')
concat(vis=[SB_no_ave_selfcal]+[f'{prefix}_LB_EB0_no_ave_selfcal_shift.ms',
                                f'{prefix}_LB_EB1_no_ave_selfcal_shift_rescaled.ms',
                                f'{prefix}_LB_EB2_no_ave_selfcal_shift_rescaled.ms',
                                f'{prefix}_LB_EB3_no_ave_selfcal_shift.ms',],
       concatvis=LB_combined, dirtol='0.1arcsec', copypointing=False)

listobs(vis=LB_combined,listfile=LB_combined+'.txt',overwrite=True)

applycal(vis=LB_combined, spw='0~23',
         gaintable=[LB_p1,LB_p2,LB_p3,LB_p4,LB_p5,LB_p6,LB_ap0,LB_ap1],
         spwmap = [LB_spw_mapping]*8,interp=['linearPD']*8,
         calwt=True, applymode='calonly',flagbackup=False)

SBLB_no_ave_selfcal = f'{prefix}_SBLB_no_ave_selfcal_time_ave.ms'
os.system(f'rm -rf {SBLB_no_ave_selfcal}*')
""" time average of 30s, tests show there is no different with data without time average """
split(vis=LB_combined, outputvis=SBLB_no_ave_selfcal,
      datacolumn='corrected', timebin = '30s', keepflags=False)

listobs(vis=SBLB_no_ave_selfcal,listfile=SBLB_no_ave_selfcal+'.txt',overwrite=True)

# Check that solutions have been applied correctly by flagging the line data, averaging and imaging continuum
# continuum has to be the same imaged in the last step of the self-cal
complete_dataset_dict = {'vis' : SBLB_no_ave_selfcal,
                         'name' : 'SBLB_concat',
                         'field' : fields['LB'],
                         'line_spws': np.array([0,2,3,
                                                4,6,7,
                                                8,10,11,
                                                12,14,15,
                                                16,18,19,
                                                20,22,23]), # list of spws containing lines
                         'line_freqs': np.array([rest_freq_13CO,rest_freq_CS,rest_freq_12CO]*6), #frequencies (Hz) corresponding to line_spws
                         'cont_spws': None,
                         'width_array': None,
                         }

# Flagchannels input string for SB_EB0: '0:837~3005, 2:792~3041, 3:789~3057'
# Flagchannels input string for SB_EB1: '0:836~3004, 2:793~3042, 3:788~3056'
# Flagchannels input string for LB_EB0: '0:833~3001, 2:797~3045, 3:781~3049'
# Flagchannels input string for LB_EB1: '0:833~3001, 2:797~3045, 3:781~3049'
# Flagchannels input string for LB_EB2: '0:833~3001, 2:797~3045, 3:781~3049'
# Flagchannels input string for LB_EB3: '0:833~3001, 2:797~3045, 3:781~3049'


#use the output of get_flagchannels at the beginning of the script to define fitspw
fitspw =  '0:837~3005, 1:0, 2:792~3041, 3:789~3057,'\
         +'4:836~3004, 5:0, 6:793~3042, 7:788~3056,'\
         +'8:833~3001, 9:0, 10:797~3045, 11:781~3049,'\
         +'12:833~3001, 13:0, 14:797~3045, 15:781~3049,'\
         +'16:833~3001, 17:0, 18:797~3045, 19:781~3049,'\
         +'20:833~3001, 21:0, 22:797~3045, 23:781~3049'

avg_cont(ms_dict=complete_dataset_dict, output_prefix=prefix, flagchannels = fitspw,
         contspws = complete_dataset_dict['cont_spws'], width_array=complete_dataset_dict['width_array'])

# image the "avg then cal" with the same parameters as in last step of self-cal
tclean_wrapper(vis=LB_cont_averaged+'.ms',
               imagename = LB_cont_averaged+'_image', mask=LB_mask,
               threshold = '0.025mJy', deconvolver='multiscale', scales=scales['LB'],
               imsize=imsize['LB'], cellsize=cellsize['LB'],
               robust=0.5, interactive=False, parallel=use_parallel, gridder='standard')
estimate_SNR(LB_cont_averaged+'_image'+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(LB_cont_averaged+'_image'+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],save_folder=calibrate_linedata_folder)
#HD_135344B_time_ave_continuum_image.image
#Beam 0.163 arcsec x 0.130 arcsec (-77.52 deg)
#Flux inside disk mask: 426.91 mJy
#Peak intensity of source: 16.58 mJy/beam
#rms: 2.33e-02 mJy/beam
#Peak SNR: 712.57

# image the "cal then avg" with the same parameters as in last step of self-cal
complete_dataset_image = prefix+'_'+complete_dataset_dict['name']+'_initcont_image'
tclean_wrapper(vis=prefix+'_'+complete_dataset_dict['name']+'_initcont.ms',
               imagename = complete_dataset_image, mask=LB_mask,
               threshold = '0.025mJy', deconvolver='multiscale', scales=scales['LB'],
               imsize=imsize['LB'], cellsize=cellsize['LB'],
               robust=0.5, interactive=False, parallel=use_parallel, gridder='standard')
estimate_SNR(complete_dataset_image+'.image', disk_mask = LB_mask, noise_mask = noise_annulus_LB)
generate_image_png(complete_dataset_image+'.image',plot_sizes=image_png_plot_sizes,
                   color_scale_limits=[-3*rms_LB,10*rms_LB],save_folder=calibrate_linedata_folder)
#HD_135344B_SBLB_concat_initcont_image.image
#Beam 0.163 arcsec x 0.130 arcsec (-77.52 deg)
#Flux inside disk mask: 426.92 mJy
#Peak intensity of source: 16.58 mJy/beam
#rms: 2.33e-02 mJy/beam
#Peak SNR: 712.34

# Plot ratio of "cal then avg" and "avg then cal". It should be equal to ~one (only difference being the time average):
ref_image = LB_cont_averaged+'_image'+'.image'
os.system('rm -rf '+complete_dataset_image+'.ratio')
immath(imagename=[ref_image,complete_dataset_image+'.image'],mode='evalexpr',
       outfile=complete_dataset_image+'.ratio',
       expr='iif(IM0 > 3*'+str(rms_LB)+', IM1/IM0, 0)'
       )
generate_image_png(f'{complete_dataset_image}.ratio',plot_sizes=[2*mask_semimajor,2*mask_semimajor],
                   color_scale_limits=[0.5,1.5],image_units='ratio',
                   save_folder=calibrate_linedata_folder)

# Do continuum subtraction
contsub_vis = f'{SBLB_no_ave_selfcal}.contsub'
os.system(f'rm -rf {contsub_vis}*')
uvcontsub(vis=SBLB_no_ave_selfcal, spw='0~23', fitspw=fitspw,
          excludechans=True, solint='int', fitorder=1, want_cont=False)

# Split final ms table into separate spws for 12CO, 13CO, CS and continuum

#12CO
vis_12CO = SBLB_no_ave_selfcal[:-3]+'_12CO.ms'
os.system(f'rm -rf {vis_12CO}*')
spw_12CO = '3,7,11,15,19,23'
split(vis=SBLB_no_ave_selfcal,outputvis=vis_12CO,spw=spw_12CO,
      datacolumn='data', keepflags=False)
split(vis=contsub_vis,outputvis=f'{vis_12CO}.contsub',spw=spw_12CO,
      datacolumn='data', keepflags=False)

#13CO
vis_13CO = SBLB_no_ave_selfcal[:-3]+'_13CO.ms'
os.system(f'rm -rf {vis_13CO}*')
spw_13CO = '0,4,8,12,16,20'
split(vis=SBLB_no_ave_selfcal,outputvis=vis_13CO,spw=spw_13CO,
      datacolumn='data', keepflags=False)
split(vis=contsub_vis,outputvis=f'{vis_13CO}.contsub',spw=spw_13CO,
      datacolumn='data', keepflags=False)

#CS
vis_CS = SBLB_no_ave_selfcal[:-3]+'_CS.ms'
os.system(f'rm -rf {vis_CS}*')
spw_CS = '2,6,10,14,18,22'
split(vis=SBLB_no_ave_selfcal,outputvis=vis_CS,spw=spw_CS,
      datacolumn='data', keepflags=False)
split(vis=contsub_vis,outputvis=f'{vis_CS}.contsub',spw=spw_CS,
      datacolumn='data', keepflags=False)

#continuum spw
vis_continuum = SBLB_no_ave_selfcal[:-3]+'_contspw.ms'
os.system(f'rm -rf {vis_continuum}*')
spw_continuum = '1,5,9,13,17,21'
split(vis=SBLB_no_ave_selfcal,outputvis=vis_continuum,spw=spw_continuum,
      datacolumn='data', keepflags=False)
split(vis=contsub_vis,outputvis=f'{vis_continuum}.contsub',spw=spw_continuum,
      datacolumn='data', keepflags=False)
